debian/changelog

-libbiod (0.2.3+git20191120.b8eecef-1) UNRELEASED; urgency=medium
+libbiod (0.2.3+git20191120.b8eecef-1) unstable; urgency=medium
 
+  [ Andreas Tille ]
   * New upstream version
     Closes: #912077
   * debhelper-compat 12
   * Standards-Version: 4.4.1
   * libundead is not needed any more
   * Remove old patches
-  * Use Makefile provided by upstream for building
   * Rebuild to bump dependencies latest libphobos2-ldc-shared
-    Closes: 927166
+    Closes: #927166
   * Remove obsolete fields Name from debian/upstream/metadata.
-  * Force making library
 
- -- Andreas Tille <tille@debian.org>  Tue, 19 Nov 2019 14:01:46 +0100
+  [ Matthias Klumpp ]
+  * respect-env-dflags.patch: Make Makefile respect environment flags
+  * d/watch: Look for release tags only again
+  * add-meson-build.patch: Build the software with Meson
+  * Build with optimization flags from upstream
+  * Ignore test failures for now (Closes: #917721)
+  * Include a static library build
+
+ -- Matthias Klumpp <mak@debian.org>  Sun, 15 Dec 2019 12:36:12 +0100
 
 libbiod (0.2.1-1) unstable; urgency=medium
 

debian/control

@@ -5,7 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12),
                dh-dlang,
-               meson (>= 0.40),
+               meson (>= 0.48),
                pkg-config,
                zlib1g-dev
 Standards-Version: 4.4.1
@@ -16,8 +16,8 @@ Homepage: https://github.com/biod/BioD
 Package: libbiod0
 Architecture: any
 Section: libs
-Depends: ${shlibs:Depends},
-         ${misc:Depends}
+Depends: ${misc:Depends},
+         ${shlibs:Depends}
 Description: bioinformatics library in D
  BioD is a fast and memory efficient bioinformatics library written in
  the D programming language. BioD aims to:
@@ -34,9 +34,9 @@ Description: bioinformatics library in D
 Package: libbiod-dev
 Architecture: any
 Section: libdevel
-Depends: ${shlibs:Depends},
+Depends: libbiod0 (= ${binary:Version}),
          ${misc:Depends},
-         libbiod0 (= ${binary:Version})
+         ${shlibs:Depends}
 Description: bioinformatics library in D (development files)
  BioD is a fast and memory efficient bioinformatics library written in
  the D programming language. BioD aims to:

debian/libbiod-dev.install

 usr/include/d/bio/*
+usr/lib/*/libbiod.a
 usr/lib/*/libbiod.so
 usr/lib/*/pkgconfig/biod.pc

debian/patches/02_respect-env-dflags.patch

+Make the Makefile respect the environment flags Debian provides,
+to fix builds.
+--- a/Makefile
++++ b/Makefile
+@@ -2,8 +2,9 @@
+ #
+ #   make sharedlibrary  : make shared library
+ 
+-D_COMPILER=ldc2
+-DFLAGS = -wi -g -relocation-model=pic -Icontrib/undead -L-lz
++DC ?= ldc2
++DFLAGS ?= -wi -g -relocation-model=pic
++DFLAGS += -Icontrib/undead -L-lz
+ 
+ ifndef GUIX
+   ifdef GUIX_ENVIRONMENT
+@@ -34,11 +35,11 @@
+ default debug release static sharedlibrary: $(BIN)
+ 
+ %.o: %.d
+-	$(D_COMPILER) $(DFLAGS) -c $< -od=$(dir $@)
++	$(DC) $(DFLAGS) -c $< -od=$(dir $@)
+ 
+ $(BIN): $(OBJ)
+ 	$(info linking...)
+-	$(D_COMPILER) -main $(DFLAGS) $(OBJ) -of=$(BIN)
++	$(DC) -main $(DFLAGS) $(OBJ) -of=$(BIN)
+ 
+ check: $(BIN)
+ 	$(info running tests...)

debian/patches/03_add-meson-build.patch

+From 6a5a4710d4600b939e7d3ef183be73756326b4b5 Mon Sep 17 00:00:00 2001
+From: Matthias Klumpp <matthias@tenstral.net>
+Date: Sun, 15 Dec 2019 00:45:59 +0100
+Subject: [PATCH] Add Meson build definition
+
+---
+ meson.build       | 184 ++++++++++++++++++++++++++++++++++++++++++++++
+ meson_options.txt |   1 +
+ 2 files changed, 185 insertions(+)
+ create mode 100644 meson.build
+ create mode 100644 meson_options.txt
+
+diff --git a/meson.build b/meson.build
+new file mode 100644
+index 0000000..4408520
+--- /dev/null
++++ b/meson.build
+@@ -0,0 +1,184 @@
++project('BioD', 'd',
++    meson_version : '>=0.48',
++    license : 'MIT',
++    version : '0.2.3',
++    default_options : ['buildtype=debugoptimized']
++)
++
++project_soversion = '0'
++
++src_dir = include_directories('.')
++pkgc = import('pkgconfig')
++
++extra_dflags = []
++if get_option('optimize_strong')
++    if meson.get_compiler('d').get_id() == 'gcc'
++        message('No custom strong optimization flags are defined for GDC yet.')
++    endif
++    extra_dflags = ['-O3', '-release', '-enable-inlining', '-boundscheck=off']
++endif
++
++#
++# Dependencies
++#
++zlib_dep = dependency('zlib')
++
++#
++# Sources
++#
++undead_src = [
++    'contrib/undead/cstream.d',
++    'contrib/undead/doformat.d',
++    'contrib/undead/internal/file.d',
++    'contrib/undead/stream.d',
++    'contrib/undead/utf.d'
++]
++
++biod_src = [
++    'bio/core/base.d',
++    'bio/core/bgzf/block.d',
++    'bio/core/bgzf/chunk.d',
++    'bio/core/bgzf/compress.d',
++    'bio/core/bgzf/constants.d',
++    'bio/core/bgzf/inputstream.d',
++    'bio/core/bgzf/outputstream.d',
++    'bio/core/bgzf/virtualoffset.d',
++    'bio/core/call.d',
++    'bio/core/decompress.d',
++    'bio/core/genotype.d',
++    'bio/core/kmer.d',
++    'bio/core/region.d',
++    'bio/core/sequence.d',
++    'bio/core/tinymap.d',
++    'bio/core/utils/algo.d',
++    'bio/core/utils/bylinefast.d',
++    'bio/core/utils/exception.d',
++    'bio/core/utils/format.d',
++    'bio/core/utils/memoize.d',
++    'bio/core/utils/outbuffer.d',
++    'bio/core/utils/range.d',
++    'bio/core/utils/roundbuf.d',
++    'bio/core/utils/stream.d',
++    'bio/core/utils/switchendianness.d',
++    'bio/core/utils/tmpfile.d',
++    'bio/core/utils/zlib.d',
++    'bio/std/experimental/hts/bam/header.d',
++    'bio/std/experimental/hts/bam/reader.d',
++    'bio/std/experimental/hts/bam/writer.d',
++    'bio/std/experimental/hts/bgzf.d',
++    'bio/std/experimental/hts/bgzf_writer.d',
++    'bio/std/experimental/hts/constants.d',
++    'bio/std/experimental/hts/hashing.d',
++    'bio/std/experimental/hts/logger.d',
++    'bio/std/experimental/hts/pileup.d',
++    'bio/std/experimental/hts/reads.d',
++    'bio/std/experimental/hts/unpack.d',
++    'bio/std/file/fai.d',
++    'bio/std/file/fasta.d',
++    'bio/std/file/fastq.d',
++    'bio/std/genotype/maf.d',
++    'bio/std/genotype/snp.d',
++    'bio/std/hts/bam/abstractreader.d',
++    'bio/std/hts/bam/bai/bin.d',
++    'bio/std/hts/bam/baifile.d',
++    'bio/std/hts/bam/bai/indexing.d',
++    'bio/std/hts/bam/baseinfo.d',
++    'bio/std/hts/bam/cigar.d',
++    'bio/std/hts/bam/constants.d',
++    'bio/std/hts/bam/md/core.d',
++    'bio/std/hts/bam/md/operation.d',
++    'bio/std/hts/bam/md/parse.d',
++    'bio/std/hts/bam/md/reconstruct.d',
++    'bio/std/hts/bam/multireader.d',
++    'bio/std/hts/bam/pileup.d',
++    'bio/std/hts/bam/randomaccessmanager.d',
++    'bio/std/hts/bam/read.d',
++    'bio/std/hts/bam/reader.d',
++    'bio/std/hts/bam/readrange.d',
++    'bio/std/hts/bam/reference.d',
++    'bio/std/hts/bam/referenceinfo.d',
++    'bio/std/hts/bam/region.d',
++    'bio/std/hts/bam/splitter.d',
++    'bio/std/hts/bam/tagvalue.d',
++    'bio/std/hts/bam/validation/alignment.d',
++    'bio/std/hts/bam/validation/samheader.d',
++    'bio/std/hts/bam/writer.d',
++    'bio/std/hts/iontorrent/flowcall.d',
++    'bio/std/hts/iontorrent/flowindex.d',
++    'bio/std/hts/sam/header.d',
++    'bio/std/hts/sam/reader.d',
++    'bio/std/hts/sam/utils/fastrecordparser.d',
++    'bio/std/hts/sam/utils/recordparser.d',
++    'bio/std/hts/snpcallers/maq.d',
++    'bio/std/hts/snpcallers/simple.d',
++    'bio/std/hts/thirdparty/msgpack.d',
++    'bio/std/hts/utils/array.d',
++    'bio/std/hts/utils/graph.d',
++    'bio/std/hts/utils/samheadermerger.d',
++    'bio/std/hts/utils/value.d',
++    'bio/std/maf/block.d',
++    'bio/std/maf/parser.d',
++    'bio/std/maf/reader.d',
++    'bio/std/range/splitter.d',
++    'bio/std/sff/constants.d',
++    'bio/std/sff/index.d',
++    'bio/std/sff/read.d',
++    'bio/std/sff/reader.d',
++    'bio/std/sff/readrange.d',
++    'bio/std/sff/utils/roundup.d',
++    'bio/std/sff/writer.d'
++]
++
++tests_src = [
++    'test/unittests.d'
++]
++
++#
++# Includes
++#
++install_subdir('bio/', install_dir: 'include/d/bio/')
++install_subdir('contrib/undead', install_dir: 'include/d/bio/contrib/')
++
++#
++# Library and pkg-config
++#
++biod_lib = both_libraries('biod',
++        [undead_src, biod_src],
++        dependencies: [zlib_dep],
++        install: true,
++        version: meson.project_version(),
++        soversion: project_soversion,
++        d_args: extra_dflags
++)
++pkgc.generate(name: 'biod',
++              libraries: biod_lib,
++              subdirs: 'd/bio/',
++              version: meson.project_version(),
++              description: 'D library for computational biology and bioinformatics'
++)
++
++#
++# Tests
++#
++
++# workaround for GDC having no -main switch
++test_main_src = join_paths(meson.build_root(), 'utmain.d')
++run_command('sh',
++            ['-c', 'echo "void main () {}" > ' + test_main_src],
++            check: true)
++
++biod_test_exe = executable('biod_test',
++    [undead_src,
++     biod_src,
++     tests_src,
++     test_main_src],
++    dependencies: [zlib_dep],
++    d_unittest: true,
++    d_args: extra_dflags
++)
++test('biod_tests',
++     biod_test_exe,
++     args: ['--DRT-gcopt=gc:precise disable:1 cleanup:none'],
++     workdir: join_paths(meson.source_root(), 'test'),
++     is_parallel: false
++)
+diff --git a/meson_options.txt b/meson_options.txt
+new file mode 100644
+index 0000000..607da9a
+--- /dev/null
++++ b/meson_options.txt
+@@ -0,0 +1 @@
++option('optimize_strong', type : 'boolean', value: false)
+-- 
+2.24.0
+

debian/patches/series

-fix_clean_target.patch
+01_fix_clean_target.patch
+02_respect-env-dflags.patch
+03_add-meson-build.patch

debian/rules

@@ -2,13 +2,16 @@
 # DH_VERBOSE := 1
 
 include /usr/share/dh-dlang/dlang-flags.mk
-export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 %:
-	dh $@
+	dh $@ --buildsystem=meson
 
-override_dh_auto_build:
-	$(MAKE) sharedlibrary
+override_dh_auto_configure:
+	dh_auto_configure -- -Doptimize_strong=true
 
 override_dh_missing:
-	dh_missing --list-missing
+	dh_missing --fail-missing
+
+override_dh_auto_test:
+	# we ignore test failures for now, the tests fail to find a few files correctly
+	-dh_auto_test

debian/watch

 version=4
 
-# https://github.com/biod/BioD/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
-
-# just for testing
-opts="mode=git,pretty=0.2.3+git%cd.%h" \
-    https://github.com/biod/BioD.git HEAD
+https://github.com/biod/BioD/tags .*/v?(\d\S*)\.tar\.gz